Contacts of the helix formed by residues 234 - 242 (chain B) in PDB entry 3H2U
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 234 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232B PHE* 2.9 35.2 - - + -
233B ASN* 1.3 74.9 - - - +
235B VAL* 1.3 55.7 + - - +
236B ASP* 3.3 7.5 - - - +
237B ALA* 2.4 42.4 + - + +
238B LEU* 2.3 42.7 + - - +
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Residues in contact with VAL 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233B ASN* 3.8 13.7 - - - +
234B ASP* 1.3 71.8 - - - +
236B ASP* 1.3 55.4 + - - +
238B LEU* 3.9 4.9 - - + -
239B CYS* 2.6 60.0 + - - +
251B CYS 4.2 2.2 - - - +
252B GLN* 3.9 9.9 - - + -
253B LEU* 2.8 48.1 - - + +
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Residues in contact with ASP 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234B ASP* 3.3 6.9 - - - +
235B VAL* 1.3 83.1 - - - +
237B ALA* 1.3 56.9 + - - +
239B CYS* 4.1 2.3 - - - +
240B ARG* 3.0 26.9 + - - +
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Residues in contact with ALA 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234B ASP* 2.4 48.2 + - + +
235B VAL 3.3 0.2 - - - -
236B ASP* 1.3 71.9 - - - +
238B LEU* 1.3 55.3 + - - +
240B ARG* 3.0 6.8 + - - +
241B ALA* 2.7 36.2 + - - +
287B LEU* 4.3 10.8 - - + +
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Residues in contact with LEU 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B VAL* 4.8 5.8 - - + -
228B LEU* 4.0 26.2 - - + -
232B PHE* 3.3 28.0 - - + -
234B ASP* 2.3 32.9 + - - +
235B VAL* 3.9 2.9 - - + -
237B ALA* 1.3 73.3 - - - +
239B CYS* 1.3 64.7 + - - +
241B ALA* 3.4 3.0 + - - +
242B LEU* 3.0 64.4 + - + +
251B CYS* 4.3 10.3 - - - -
253B LEU* 4.6 7.2 - - + -
265B ALA* 4.1 20.9 - - + -
267B LEU* 4.7 0.2 - - + -
287B LEU* 4.1 11.8 - - + +
292B LEU* 5.1 5.4 - - + -
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Residues in contact with CYS 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B VAL* 2.6 50.8 + - - +
236B ASP* 4.4 2.7 - - - +
238B LEU* 1.3 73.0 - - - +
240B ARG* 1.3 55.1 + - - +
242B LEU* 3.4 8.3 + - - +
243B SER* 2.5 30.0 + - - -
248B PRO* 4.2 4.4 - - + +
251B CYS* 2.0 54.3 - - + -
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Residues in contact with ARG 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B ASP 3.0 20.5 + - - +
237B ALA* 3.0 9.8 + - - +
239B CYS* 1.3 73.5 - - - +
241B ALA* 1.3 68.5 + - - +
243B SER* 2.9 29.2 + - - -
244B ALA* 3.9 4.3 + - - +
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Residues in contact with ALA 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B ALA 2.7 16.3 + - - +
238B LEU 3.5 9.4 - - - +
240B ARG* 1.3 72.9 - - - +
242B LEU* 1.3 62.1 + - + +
243B SER 3.1 5.5 + - - -
244B ALA* 3.4 19.6 + - - +
281B GLN* 4.3 6.4 + - - +
282B ALA* 5.6 1.0 - - - +
285B LEU* 4.5 20.3 - - + +
287B LEU* 4.1 18.8 - - + -
292B LEU* 6.4 1.1 - - + -
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Residues in contact with LEU 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B LEU* 6.1 2.2 - - + -
225B VAL* 3.8 25.6 - - + -
238B LEU* 3.0 45.4 + - + +
239B CYS 4.0 2.9 - - - +
240B ARG 3.1 1.6 - - - -
241B ALA* 1.3 79.1 - - + +
243B SER* 1.3 59.3 + - - +
244B ALA 3.5 1.1 - - - -
245B VAL* 5.0 1.4 + - - +
246B HIS 3.4 7.4 - - - +
248B PRO* 3.9 1.6 - - - +
267B LEU* 3.6 22.0 - - + -
269B TYR* 3.0 31.1 + - - +
278B ALA* 4.6 6.3 - - + +
281B GLN* 5.6 1.1 - - - -
282B ALA* 3.4 32.1 - - + -
292B LEU* 6.0 3.6 - - + -
294B VAL* 4.6 4.7 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il